Merge branch 'feature-miniconda_support' into develop

src/plugins/__init__.py

@@ -5,13 +5,14 @@ from __future__ import unicode_literals
 from __future__ import division
 from __future__ import absolute_import
 
+import importlib
+import pkgutil
+
+
 __author__ = 'Ingo Heimbach'
 __email__ = 'i.heimbach@fz-juelich.de'
 
 
-import importlib
-import pkgutil
-
 _modules = None
 _ext2module = None
 
@@ -23,6 +24,7 @@ def _normalize_ext(f):
         return f(file_ext, *args, **kwargs)
     return g
 
+
 def _check_ext_availability(f):
     @_normalize_ext
     def g(file_ext, *args, **kwargs):
@@ -35,6 +37,7 @@ def _check_ext_availability(f):
             raise NotInitializedError
     return g
 
+
 class NotInitializedError(Exception):
     pass
 
@@ -50,14 +53,17 @@ def add_plugin_command_line_arguments(parser):
                 name_or_flags = [name_or_flags]
             parser.add_argument(*name_or_flags, **kwargs)
 
+
 @_check_ext_availability
 def parse_command_line_arguments(file_ext, arguments):
     return _ext2module[file_ext].parse_command_line_arguments(arguments)
 
+
 @_check_ext_availability
 def pre_create_app(file_ext, **arguments):
     return _ext2module[file_ext].pre_create_app(**arguments)
 
+
 @_normalize_ext
 def setup_startup(file_ext, app_path, executable_path, app_executable_path,
                   executable_root_path, macos_path, resources_path):
@@ -72,10 +78,12 @@ def setup_startup(file_ext, app_path, executable_path, app_executable_path,
     else:
         raise NotInitializedError
 
+
 @_check_ext_availability
 def post_create_app(file_ext, **arguments):
     return _ext2module[file_ext].post_create_app(**arguments)
 
+
 def _pkg_init():
     global _modules, _ext2module
 

src/plugins/python.py

@@ -5,9 +5,6 @@ from __future__ import unicode_literals
 from __future__ import division
 from __future__ import absolute_import
 
-__author__ = 'Ingo Heimbach'
-__email__ = 'i.heimbach@fz-juelich.de'
-
 import fnmatch
 import itertools
 import os
@@ -15,10 +12,13 @@ import re
 import shutil
 import subprocess
 from jinja2 import Template
-from .util import libpatch
 from .util import command
 
 
+__author__ = 'Ingo Heimbach'
+__email__ = 'i.heimbach@fz-juelich.de'
+
+
 PY_PRE_STARTUP_CONDA_SETUP = '''
 #!/bin/bash
 SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
@@ -74,46 +74,45 @@ _CONDA_DEFAULT_PACKAGES = ('pyobjc-framework-cocoa', )
 _CONDA_DEFAULT_CHANNELS = ('https://conda.binstar.org/erik', )
 _EXT_PYLIB_VARIABLE = 'PYLIBPATH'
 _EXT_MAKEFILE_TARGET = 'app_extension_modules'
-_GR_LIB_COPY_DICT = {'/opt/X11/lib': 'lib/X11'}
-_GR_LIB_DIR_PATHS_TO_PATCH = ('lib/X11', 'lib/python2.7/site-packages/gr', 'lib/python2.7/site-packages/gr3')
-_GR_OLD_TO_NEW_DEPENDENCY_DICT = {'/opt/X11/': '@executable_path/../lib/X11/',
-                                  '/usr/local/qt-4.8/lib/': '@executable_path/../lib/'}
-# TODO: add support for more libraries, for example wxWidgets
 
 
 _create_conda_env = False
 _requirements_file = None
 _conda_channels = None
 _extension_makefile = None
-_conda_gr_included = False
 
 
 class CondaError(Exception):
     pass
 
+
 class LibPatchingError(Exception):
     pass
 
+
 class ExtensionModuleError(Exception):
     pass
 
 
 def get_command_line_arguments():
     arguments = [(('--conda', ), {'dest': 'conda_req_file', 'action': 'store', 'type': os.path.abspath,
-                                  'help': 'Creates a miniconda environment from the given conda requirements file and includes it in the app bundle. Can be used to create self-contained python apps.'}),
+                                  'help': 'Creates a miniconda environment from the given conda requirements file '
+                                          'and includes it in the app bundle. Can be used to create self-contained '
+                                          'python apps.'}),
                  (('--conda-channels', ), {'dest': 'conda_channels', 'action': 'store', 'nargs': '+',
-                                           'help': 'A list of custom conda channels to install packages that are not included in the main anaconda distribution.'}),
+                                           'help': 'A list of custom conda channels to install packages that are not '
+                                                   'included in the main anaconda distribution.'}),
                  (('--extension-makefile', ), {'dest': 'extension_makefile', 'action': 'store', 'type': os.path.abspath,
-                                               'help': 'Path to a makefile for building python extension modules. The makefile is called with the target "{target}" and a variable "{libvariable}" that holds the path to the conda python library.'.format(target=_EXT_MAKEFILE_TARGET, libvariable=_EXT_PYLIB_VARIABLE)})]
+                                               'help': 'Path to a makefile for building python extension modules. The '
+                                                       'makefile is called with the target "{target}" and a variable '
+                                                       '"{libvariable}" that holds the path to the conda python '
+                                                       'library.'.format(target=_EXT_MAKEFILE_TARGET,
+                                                                         libvariable=_EXT_PYLIB_VARIABLE)})]
     return arguments
 
-def parse_command_line_arguments(args):
-    global _create_conda_env, _requirements_file, _conda_channels, _extension_makefile, _conda_gr_included
 
-    def is_gr_in_conda_requirements(requirements_file):
-        with open(requirements_file, 'r') as f:
-            found_gr = any((line.startswith('gr=') for line in f))
-        return found_gr
+def parse_command_line_arguments(args):
+    global _create_conda_env, _requirements_file, _conda_channels, _extension_makefile
 
     checked_args = {}
     if args.conda_req_file is not None:
@@ -124,12 +123,13 @@ def parse_command_line_arguments(args):
             _conda_channels = args.conda_channels
         if args.extension_makefile is not None:
             _extension_makefile = args.extension_makefile
-        _conda_gr_included = is_gr_in_conda_requirements(_requirements_file)
     return checked_args
 
+
 def pre_create_app(**kwargs):
     pass
 
+
 def setup_startup(app_path, executable_path, app_executable_path, executable_root_path, macos_path, resources_path):
     def create_python_startup_script(main_module):
         template = Template(PY_STARTUP_SCRIPT)
@@ -144,7 +144,8 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
         python_lib_pathes = tuple(['{lib_dir_path}/{path}'.format(lib_dir_path=lib_dir_path, path=path)
                                    for path in os.listdir(lib_dir_path) if fnmatch.fnmatch(path, lib_pattern)])
         for python_lib_path in python_lib_pathes:
-            rel_python_lib_path = '@executable_path/{rel_path}'.format(rel_path=os.path.relpath(python_lib_path, python_dir_path))
+            rel_python_lib_path = '@executable_path/{rel_path}'.format(rel_path=os.path.relpath(python_lib_path,
+                                                                                                python_dir_path))
             with open(os.devnull, 'w') as dummy:
                 try:
                     subprocess.check_call(['install_name_tool', '-id', rel_python_lib_path, python_lib_path],
@@ -159,13 +160,14 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
                 env_path = '{resources}/{env}'.format(resources=resources_path, env='conda_env')
                 try:
                     subprocess.check_call(['conda', 'create', '-p', env_path,
-                                           '--file', _requirements_file, '--copy', '--quiet', '--yes']
-                                          + list(itertools.chain(*[('-c', channel) for channel in conda_channels])),
+                                           '--file', _requirements_file, '--copy', '--quiet', '--yes'] +
+                                          list(itertools.chain(*[('-c', channel) for channel in conda_channels])),
                                           stdout=dummy, stderr=dummy)
-                    subprocess.check_call(' '.join(['source', '{env_path}/bin/activate'.format(env_path=env_path), env_path, ';',
-                                                    'conda', 'install', '--copy', '--quiet', '--yes']
-                                                   + list(_CONDA_DEFAULT_PACKAGES)
-                                                   + list(itertools.chain(*[('-c', channel) for channel in _CONDA_DEFAULT_CHANNELS]))),
+                    subprocess.check_call(' '.join(['source', '{env_path}/bin/activate'.format(env_path=env_path),
+                                                    env_path, ';', 'conda', 'install', '--copy', '--quiet', '--yes'] +
+                                                   list(_CONDA_DEFAULT_PACKAGES) +
+                                                   list(itertools.chain(*[('-c', channel)
+                                                                          for channel in _CONDA_DEFAULT_CHANNELS]))),
                                           stdout=dummy, stderr=dummy, shell=True)
                 except subprocess.CalledProcessError:
                     raise CondaError('The conda environment could not be installed.')
@@ -184,8 +186,10 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
             for root_path, dirnames, filenames in os.walk(env_path):
                 dirpaths = [os.path.join(root_path, dirname) for dirname in dirnames]
                 filepaths = [os.path.join(root_path, filename) for filename in filenames]
-                link_dirpaths = [dirpath for dirpath in dirpaths if os.path.islink(dirpath) and not os.path.realpath(dirpath).startswith(env_path)]
-                link_filepaths = [filepath for filepath in filepaths if os.path.islink(filepath) and not os.path.realpath(filepath).startswith(env_path)]
+                link_dirpaths = [dirpath for dirpath in dirpaths if os.path.islink(dirpath) and
+                                 not os.path.realpath(dirpath).startswith(env_path)]
+                link_filepaths = [filepath for filepath in filepaths if os.path.islink(filepath) and
+                                  not os.path.realpath(filepath).startswith(env_path)]
                 for link_dirpath in link_dirpaths:
                     real_dirpath = os.path.realpath(link_dirpath)
                     os.remove(link_dirpath)
@@ -198,7 +202,8 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
         def fix_activate_script():
             SEARCHED_LINE_START = '_THIS_DIR='
             INSERT_LINE = 'export PATH=${_THIS_DIR}:${PATH}'
-            full_conda_activate_path = '{env_path}/{conda_activate_path}'.format(env_path=env_path, conda_activate_path=CONDA_ACTIVATE_PATH)
+            full_conda_activate_path = '{env_path}/{conda_activate_path}'.format(env_path=env_path,
+                                                                                 conda_activate_path=CONDA_ACTIVATE_PATH)
             found_line = False
             new_lines = []
             with open(full_conda_activate_path, 'r') as f:
@@ -250,18 +255,6 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
         fix_conda_shebang()
         copy_missing_conda_packages()
 
-    def fix_conda_gr(env_path):
-        def copy_missing_dependencies():
-            for src, dst in _GR_LIB_COPY_DICT.iteritems():
-                shutil.copytree(src, '{env_path}/{relative_dst}'.format(env_path=env_path, relative_dst=dst))
-
-        def patch_lib_dependencies():
-            lib_dir_paths = tuple(('{env_path}/{relative_lib_path}'.format(env_path=env_path, relative_lib_path=lib_path) for lib_path in _GR_LIB_DIR_PATHS_TO_PATCH))
-            libpatch.patch_libs(lib_dir_paths, _GR_OLD_TO_NEW_DEPENDENCY_DICT)
-
-        copy_missing_dependencies()
-        patch_lib_dependencies()
-
     def build_extension_modules(env_path):
         def get_makefile_path():
             if executable_root_path is not None and \
@@ -292,8 +285,6 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
     if _create_conda_env:
         env_path = create_conda_env()
         make_conda_portable(env_path)
-        if _conda_gr_included:
-            fix_conda_gr(env_path)
         if _extension_makefile is not None:
             build_extension_modules(env_path)
         env_startup_script = PY_PRE_STARTUP_CONDA_SETUP
@@ -305,5 +296,6 @@ def setup_startup(app_path, executable_path, app_executable_path, executable_roo
 
     return new_executable_path
 
+
 def post_create_app(**kwargs):
     pass

src/plugins/util/command.py

@@ -5,10 +5,12 @@ from __future__ import unicode_literals
 from __future__ import division
 from __future__ import absolute_import
 
+import subprocess
+
+
 __author__ = 'Ingo Heimbach'
 __email__ = 'i.heimbach@fz-juelich.de'
 
-import subprocess
 
 def exec_cmd(*cmd):
     cmd = ' '.join(cmd)
@@ -16,5 +18,6 @@ def exec_cmd(*cmd):
     stdout, stderr = p.communicate()
     return stdout
 
+
 def which(cmd):
     return exec_cmd('which', cmd).strip()

src/plugins/util/libpatch.py

@@ -5,9 +5,6 @@ from __future__ import unicode_literals
 from __future__ import division
 from __future__ import absolute_import
 
-__author__ = 'Ingo Heimbach'
-__email__ = 'i.heimbach@fz-juelich.de'
-
 import logging
 import os
 import os.path
@@ -15,6 +12,10 @@ import re
 from .command import exec_cmd
 
 
+__author__ = 'Ingo Heimbach'
+__email__ = 'i.heimbach@fz-juelich.de'
+
+
 def extract_dependencies(lib_path, dependency_path_prefix):
     dependency_output = exec_cmd('otool -L', lib_path)
     dependencies = []
@@ -25,6 +26,7 @@ def extract_dependencies(lib_path, dependency_path_prefix):
             dependencies.append(current_dependency)
     return dependencies
 
+
 def replace_install_name(lib_path, new_install_name_prefix):
     lib_name = os.path.basename(lib_path)
     new_install_name = '{new_install_name_prefix}{lib_name}'.format(new_install_name_prefix=new_install_name_prefix,
@@ -32,6 +34,7 @@ def replace_install_name(lib_path, new_install_name_prefix):
     logging.debug('set new install name {name}'.format(name=new_install_name))
     exec_cmd('install_name_tool -id', new_install_name, lib_path)
 
+
 def replace_dependency(lib_path, old_dependency, new_dependency_prefix):
     old_dependency_lib_name = os.path.basename(old_dependency)
     new_dependency = '{new_dependency_prefix}{lib_name}'.format(new_dependency_prefix=new_dependency_prefix,
@@ -39,17 +42,20 @@ def replace_dependency(lib_path, old_dependency, new_dependency_prefix):
     logging.debug('replace dependency {old_dep} with {new_dep}'.format(old_dep=old_dependency, new_dep=new_dependency))
     exec_cmd('install_name_tool -change', old_dependency, new_dependency, lib_path)
 
+
 def patch_lib(lib_path, old_dependency_prefix, new_dependency_prefix):
     logging.debug('patching library {lib}'.format(lib=lib_path))
-    lib_name = os.path.basename(lib_path)
+    # lib_name = os.path.basename(lib_path)
     lib_dependencies = extract_dependencies(lib_path, old_dependency_prefix)
     # replace_install_name(lib_path, new_dependency_prefix) # it is not necessary to change the install name
     for dependency in lib_dependencies:
         replace_dependency(lib_path, dependency, new_dependency_prefix)
 
+
 def list_libs_from_directory(dir_path):
     return tuple((os.path.join(dir_path, lib) for lib in os.listdir(dir_path) if re.match('.+\.((dylib)|(so))', lib)))
 
+
 def patch_libs(lib_dir_paths, old_to_new_dependency_prefix_dict):
     for lib_dir_path in lib_dir_paths:
         logging.debug('current library directory: {lib_dir_path}'.format(lib_dir_path=lib_dir_path))

src/shallow-appify.py

@@ -6,15 +6,10 @@ from __future__ import unicode_literals
 from __future__ import division
 from __future__ import absolute_import
 
-__author__ = 'Ingo Heimbach'
-__email__ = 'i.heimbach@fz-juelich.de'
-
-__version_info__ = (0, 1, 1)
-__version__ = '.'.join(map(str, __version_info__))
-
 import argparse
 import os
 import os.path
+import plugins
 import re
 import shutil
 import subprocess
@@ -25,7 +20,12 @@ from PIL import Image
 import logging
 logging.basicConfig(level=logging.WARNING)
 
-import plugins
+
+__author__ = 'Ingo Heimbach'
+__email__ = 'i.heimbach@fz-juelich.de'
+
+__version_info__ = (0, 1, 1)
+__version__ = '.'.join(map(str, __version_info__))
 
 
 INFO_PLIST_TEMPLATE = '''
@@ -107,9 +107,11 @@ class Arguments(object):
 class MissingIconError(Exception):
     pass
 
+
 class AppAlreadyExistingError(Exception):
     pass
 
+
 class InvalidAppPath(Exception):
     pass
 
@@ -119,12 +121,15 @@ def parse_args():
         parser = argparse.ArgumentParser(description='''
         Creates a runnable application for Mac OS X with references to
         system libraries. The result is a NON-self-contained app bundle.''')
-        parser.add_argument('-d', '--executable-directory', dest='executable_root_path', action='store', type=os.path.abspath,
+        parser.add_argument('-d', '--executable-directory', dest='executable_root_path', action='store',
+                            type=os.path.abspath,
                             help='Defines the executable root directory that will be included in the app.')
         parser.add_argument('-i', '--icon', dest='icon_path', action='store', type=os.path.abspath,
-                            help='Image file that is used for app icon creation. It must be quadratic with a resolution of 1024x1024 pixels or more.')
+                            help='Image file that is used for app icon creation. It must be quadratic with a '
+                                 'resolution of 1024x1024 pixels or more.')
         parser.add_argument('-e', '--environment', dest='environment_vars', action='store', nargs='+',
-                            help='Specifies which environment variables -- set on the current interpreter startup -- shall be included in the app bundle.')
+                            help='Specifies which environment variables -- set on the current interpreter startup -- '
+                                 ' shall be included in the app bundle.')
         parser.add_argument('-o', '--output', dest='app_path', action='store', type=os.path.abspath,
                             help='Sets the path the app will be saved to.')
         parser.add_argument('-v', '--version', dest='version_string', action='store',
@@ -157,7 +162,8 @@ def parse_args():
     if args.app_path is not None:
         checked_args['app_path'] = args.app_path
     else:
-        checked_args['app_path'] = '{basename_without_ext}.app'.format(basename_without_ext=os.path.splitext(os.path.basename(os.path.abspath(args.executable_path)))[0])
+        basename_without_ext = os.path.splitext(os.path.basename(os.path.abspath(args.executable_path)))[0]
+        checked_args['app_path'] = '{basename_without_ext}.app'.format(basename_without_ext=basename_without_ext)
     if args.version_string is not None:
         checked_args['version_string'] = args.version_string
     else:
@@ -170,7 +176,9 @@ def parse_args():
     args.update(plugin_args)
     return Arguments(**args)
 
-def create_info_plist_content(app_name, version, executable_path, executable_root_path=None, icon_path=None, environment_vars=None):
+
+def create_info_plist_content(app_name, version, executable_path, executable_root_path=None, icon_path=None,
+                              environment_vars=None):
     def get_short_version(version):
         match_obj = re.search('\d+(\.\d+){0,2}', version)
         if match_obj is not None:
@@ -204,19 +212,22 @@ def create_info_plist_content(app_name, version, executable_path, executable_roo
 
     return info_plist
 
+
 def create_icon_set(icon_path, iconset_out_path):
     with TemporaryDirectory() as tmp_dir:
         tmp_icns_dir = '{tmp_dir}/icon.iconset'.format(tmp_dir=tmp_dir)
         os.mkdir(tmp_icns_dir)
         original_icon = Image.open(icon_path)
         for name, size in (('icon_{size}x{size}{suffix}.png'.format(size=size, suffix=suffix), factor*size)
-                                for size in (16, 32, 128, 256, 512)
-                                    for factor, suffix in ((1, ''), (2, '@2x'))):
+                           for size in (16, 32, 128, 256, 512)
+                           for factor, suffix in ((1, ''), (2, '@2x'))):
             resized_icon = original_icon.resize((size, size), Image.ANTIALIAS)
             resized_icon.save('{icns_dir}/{icon_name}'.format(icns_dir=tmp_icns_dir, icon_name=name))
         subprocess.call(('iconutil', '--convert', 'icns', tmp_icns_dir, '--output', iconset_out_path))
 
-def create_app(app_path, version_string, executable_path, executable_root_path=None, icon_path=None, environment_vars=None, **kwargs):
+
+def create_app(app_path, version_string, executable_path, executable_root_path=None, icon_path=None,
+               environment_vars=None, **kwargs):
     def abs_path(relative_bundle_path, base=None):
         return os.path.abspath('{app_path}/{dir}'.format(app_path=base or app_path, dir=relative_bundle_path))
 
@@ -227,13 +238,13 @@ def create_app(app_path, version_string, executable_path, executable_root_path=N
             raise InvalidAppPath('The specified app path is a subpath of the source root directory.')
 
     def write_info_plist():
-        info_plist_content = create_info_plist_content(app_name, version_string, app_executable_path, executable_root_path,
-                                                       bundle_icon_path, environment_vars)
-        with open(abs_path('Info.plist', contents_path) , 'w') as f:
+        info_plist_content = create_info_plist_content(app_name, version_string, app_executable_path,
+                                                       executable_root_path, bundle_icon_path, environment_vars)
+        with open(abs_path('Info.plist', contents_path), 'w') as f:
             f.writelines(info_plist_content.encode('utf-8'))
 
     def write_pkg_info():
-        with open(abs_path('PkgInfo', contents_path) , 'w') as f:
+        with open(abs_path('PkgInfo', contents_path), 'w') as f:
             f.write(PKG_INFO_CONTENT)
 
     def copy_source():
@@ -273,6 +284,7 @@ def create_app(app_path, version_string, executable_path, executable_root_path=N
     write_pkg_info()
     set_file_permissions()
 
+
 def main():
     args = parse_args()
     try: